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Package 181/671HostnameOS / ArchBUILDCHECKBUILD BIN
DiffBind 1.6.2
Rory Stark
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DiffBind
Last Changed Rev: 76027 / Revision: 76155
Last Changed Date: 2013-04-25 07:39:24 -0700 (Thu, 25 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: DiffBind
Version: 1.6.2
Command: rm -rf DiffBind.buildbin-libdir && mkdir DiffBind.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DiffBind_1.6.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DiffBind.buildbin-libdir
StartedAt: 2013-05-01 12:19:03 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:19:29 -0700 (Wed, 01 May 2013)
EllapsedTime: 26.8 seconds
RetCode: 0
Status:  OK 
PackageFile: DiffBind_1.6.2.tgz
PackageFileSize: 1.957 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DiffBind.buildbin-libdir DiffBind_1.6.2.tar.gz'
>>>>>>> 

* installing *source* package 'DiffBind' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bamReader.cpp -o bamReader.o
In file included from bamReader.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                data = (uint8_t*)realloc(data, m_data);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        b->data = (uint8_t*)calloc(b->data_len, 1);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
bamReader.cpp:46:15: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
      right = bam_calend(&(_seq->core),bam1_cigar(_seq));
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bedReader.cpp -o bedReader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c croi_func.cpp -o croi_func.o
croi_func.cpp:38:3: warning: delete called on 'bode::IntervalSet' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
  delete isets;
  ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c croi_main.cpp -o croi_main.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c interval.cpp -o interval.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c intervalNode.cpp -o intervalNode.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c intervalSet.cpp -o intervalSet.o
intervalSet.cpp:50:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  return chroms->size();
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c intervalTree.cpp -o intervalTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mergeOne.c -o mergeOne.o
mergeOne.c:80:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  srcScores = (double **) R_alloc(cols,sizeof(double *));
                          ˜˜˜˜˜˜˜ ^˜˜˜
mergeOne.c:81:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  destScores = (double **) R_alloc(cols,sizeof(double *));
                           ˜˜˜˜˜˜˜ ^˜˜˜
mergeOne.c:148:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  srcScores = (double **) R_alloc(cols,sizeof(double *));
                          ˜˜˜˜˜˜˜ ^˜˜˜
mergeOne.c:149:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  destScores = (double **) R_alloc(cols,sizeof(double *));
                           ˜˜˜˜˜˜˜ ^˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c reader.cpp -o reader.o
In file included from reader.cpp:6:
In file included from ./bamReader.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                data = (uint8_t*)realloc(data, m_data);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        b->data = (uint8_t*)calloc(b->data_len, 1);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
reader.cpp:25:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  if (filename.compare(flen-4,4,".bam") == 0) {
      ˜˜˜˜˜˜˜˜         ˜˜˜˜^˜
reader.cpp:27:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  } else if (filename.compare(flen-4,4,".bed") == 0) {
             ˜˜˜˜˜˜˜˜         ˜˜˜˜^˜
reader.cpp:29:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  } else if (filename.compare(flen-7,7,".bed.gz") == 0) {
             ˜˜˜˜˜˜˜˜         ˜˜˜˜^˜
reader.cpp:24:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  flen = filename.length();
       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sequence.cpp -o sequence.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c util.cpp -o util.o
util.cpp:32:7: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  n = strlen(str);
    ˜ ^˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DiffBind.so bamReader.o bedReader.o croi_func.o croi_main.o interval.o intervalNode.o intervalSet.o intervalTree.o mergeOne.o reader.o sequence.o util.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DiffBind.buildbin-libdir/DiffBind/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffBind)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"